
<!doctype html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html><head><title>Python: module src.aa</title>
</head><body bgcolor="#f0f0f8">

<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="heading">
<tr bgcolor="#7799ee">
<td valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial">&nbsp;<br><big><big><strong><a href="src.html"><font color="#ffffff">src</font></a>.aa</strong></big></big> (28 December 2006)</font></td
><td align=right valign=bottom
><font color="#ffffff" face="helvetica, arial"><a href=".">index</a><br><a href="file:/user/yhuang/pdb2pqr/trunk/pdb2pqr/src/aa.py">/user/yhuang/pdb2pqr/trunk/pdb2pqr/src/aa.py</a></font></td></tr></table>
    <p><tt><a href="#Amino">Amino</a>&nbsp;Acid&nbsp;Structures&nbsp;for&nbsp;PDB2PQR<br>
&nbsp;<br>
This&nbsp;module&nbsp;contains&nbsp;the&nbsp;base&nbsp;amino&nbsp;acid&nbsp;structures&nbsp;for<br>
pdb2pqr.<br>
&nbsp;<br>
----------------------------<br>
&nbsp;<br>
PDB2PQR&nbsp;--&nbsp;An&nbsp;automated&nbsp;pipeline&nbsp;for&nbsp;the&nbsp;setup,&nbsp;execution,&nbsp;and&nbsp;analysis&nbsp;of<br>
Poisson-Boltzmann&nbsp;electrostatics&nbsp;calculations<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;Copyright&nbsp;(c)&nbsp;2002-2010,&nbsp;Jens&nbsp;Erik&nbsp;Nielsen,&nbsp;University&nbsp;College&nbsp;Dublin;&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;Nathan&nbsp;A.&nbsp;Baker,&nbsp;Washington&nbsp;University&nbsp;in&nbsp;St.&nbsp;Louis;&nbsp;Paul&nbsp;Czodrowski&nbsp;&amp;&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;Gerhard&nbsp;Klebe,&nbsp;University&nbsp;of&nbsp;Marburg<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;All&nbsp;rights&nbsp;reserved.<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;Redistribution&nbsp;and&nbsp;use&nbsp;in&nbsp;source&nbsp;and&nbsp;binary&nbsp;forms,&nbsp;with&nbsp;or&nbsp;without&nbsp;modification,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;are&nbsp;permitted&nbsp;provided&nbsp;that&nbsp;the&nbsp;following&nbsp;conditions&nbsp;are&nbsp;met:<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*&nbsp;Redistributions&nbsp;of&nbsp;source&nbsp;code&nbsp;must&nbsp;retain&nbsp;the&nbsp;above&nbsp;copyright&nbsp;notice,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;this&nbsp;list&nbsp;of&nbsp;conditions&nbsp;and&nbsp;the&nbsp;following&nbsp;disclaimer.<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*&nbsp;Redistributions&nbsp;in&nbsp;binary&nbsp;form&nbsp;must&nbsp;reproduce&nbsp;the&nbsp;above&nbsp;copyright&nbsp;notice,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;this&nbsp;list&nbsp;of&nbsp;conditions&nbsp;and&nbsp;the&nbsp;following&nbsp;disclaimer&nbsp;in&nbsp;the&nbsp;documentation&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;and/or&nbsp;other&nbsp;materials&nbsp;provided&nbsp;with&nbsp;the&nbsp;distribution.<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*&nbsp;Neither&nbsp;the&nbsp;names&nbsp;of&nbsp;University&nbsp;College&nbsp;Dublin,&nbsp;Washington&nbsp;University&nbsp;in&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;St.&nbsp;Louis,&nbsp;or&nbsp;University&nbsp;of&nbsp;Marburg&nbsp;nor&nbsp;the&nbsp;names&nbsp;of&nbsp;its&nbsp;contributors&nbsp;may&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;be&nbsp;used&nbsp;to&nbsp;endorse&nbsp;or&nbsp;promote&nbsp;products&nbsp;derived&nbsp;from&nbsp;this&nbsp;software&nbsp;without&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;specific&nbsp;prior&nbsp;written&nbsp;permission.<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;THIS&nbsp;SOFTWARE&nbsp;IS&nbsp;PROVIDED&nbsp;BY&nbsp;THE&nbsp;COPYRIGHT&nbsp;HOLDERS&nbsp;AND&nbsp;CONTRIBUTORS&nbsp;"AS&nbsp;IS"&nbsp;AND&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;ANY&nbsp;EXPRESS&nbsp;OR&nbsp;IMPLIED&nbsp;WARRANTIES,&nbsp;INCLUDING,&nbsp;BUT&nbsp;NOT&nbsp;LIMITED&nbsp;TO,&nbsp;THE&nbsp;IMPLIED&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;WARRANTIES&nbsp;OF&nbsp;MERCHANTABILITY&nbsp;AND&nbsp;FITNESS&nbsp;FOR&nbsp;A&nbsp;PARTICULAR&nbsp;PURPOSE&nbsp;ARE&nbsp;DISCLAIMED.&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;IN&nbsp;NO&nbsp;EVENT&nbsp;SHALL&nbsp;THE&nbsp;COPYRIGHT&nbsp;OWNER&nbsp;OR&nbsp;CONTRIBUTORS&nbsp;BE&nbsp;LIABLE&nbsp;FOR&nbsp;ANY&nbsp;DIRECT,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;INDIRECT,&nbsp;INCIDENTAL,&nbsp;SPECIAL,&nbsp;EXEMPLARY,&nbsp;OR&nbsp;CONSEQUENTIAL&nbsp;DAMAGES&nbsp;(INCLUDING,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;BUT&nbsp;NOT&nbsp;LIMITED&nbsp;TO,&nbsp;PROCUREMENT&nbsp;OF&nbsp;SUBSTITUTE&nbsp;GOODS&nbsp;OR&nbsp;SERVICES;&nbsp;LOSS&nbsp;OF&nbsp;USE,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;DATA,&nbsp;OR&nbsp;PROFITS;&nbsp;OR&nbsp;BUSINESS&nbsp;INTERRUPTION)&nbsp;HOWEVER&nbsp;CAUSED&nbsp;AND&nbsp;ON&nbsp;ANY&nbsp;THEORY&nbsp;OF&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;LIABILITY,&nbsp;WHETHER&nbsp;IN&nbsp;CONTRACT,&nbsp;STRICT&nbsp;LIABILITY,&nbsp;OR&nbsp;TORT&nbsp;(INCLUDING&nbsp;NEGLIGENCE&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;OR&nbsp;OTHERWISE)&nbsp;ARISING&nbsp;IN&nbsp;ANY&nbsp;WAY&nbsp;OUT&nbsp;OF&nbsp;THE&nbsp;USE&nbsp;OF&nbsp;THIS&nbsp;SOFTWARE,&nbsp;EVEN&nbsp;IF&nbsp;ADVISED&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;OF&nbsp;THE&nbsp;POSSIBILITY&nbsp;OF&nbsp;SUCH&nbsp;DAMAGE.<br>
&nbsp;<br>
----------------------------</tt></p>
<p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#aa55cc">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Modules</strong></big></font></td></tr>
    
<tr><td bgcolor="#aa55cc"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%"><table width="100%" summary="list"><tr><td width="25%" valign=top><a href="copy.html">copy</a><br>
<a href="math.html">math</a><br>
</td><td width="25%" valign=top><a href="os.html">os</a><br>
<a href="string.html">string</a><br>
</td><td width="25%" valign=top><a href="sys.html">sys</a><br>
</td><td width="25%" valign=top></td></tr></table></td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ee77aa">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Classes</strong></big></font></td></tr>
    
<tr><td bgcolor="#ee77aa"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%"><dl>
<dt><font face="helvetica, arial"><a href="src.structures.html#Residue">src.structures.Residue</a>
</font></dt><dd>
<dl>
<dt><font face="helvetica, arial"><a href="src.aa.html#Amino">Amino</a>
</font></dt><dd>
<dl>
<dt><font face="helvetica, arial"><a href="src.aa.html#ALA">ALA</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.aa.html#ARG">ARG</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.aa.html#ASN">ASN</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.aa.html#ASP">ASP</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.aa.html#CYS">CYS</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.aa.html#GLN">GLN</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.aa.html#GLU">GLU</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.aa.html#GLY">GLY</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.aa.html#HIS">HIS</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.aa.html#ILE">ILE</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.aa.html#LEU">LEU</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.aa.html#LYS">LYS</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.aa.html#MET">MET</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.aa.html#PHE">PHE</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.aa.html#PRO">PRO</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.aa.html#SER">SER</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.aa.html#THR">THR</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.aa.html#TRP">TRP</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.aa.html#TYR">TYR</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.aa.html#VAL">VAL</a>
</font></dt></dl>
</dd>
<dt><font face="helvetica, arial"><a href="src.aa.html#LIG">LIG</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.aa.html#WAT">WAT</a>
</font></dt></dl>
</dd>
</dl>
 <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="ALA">class <strong>ALA</strong></a>(<a href="src.aa.html#Amino">Amino</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Alanine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Alanine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.aa.html#ALA">ALA</a></dd>
<dd><a href="src.aa.html#Amino">Amino</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="ALA-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<hr>
Methods inherited from <a href="src.aa.html#Amino">Amino</a>:<br>
<dl><dt><a name="ALA-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="ALA-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="ALA-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Override&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;version&nbsp;of<br>
<a href="#ALA-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list).</tt></dd></dl>

<dl><dt><a name="ALA-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;name&nbsp;to&nbsp;use&nbsp;for&nbsp;the&nbsp;forcefield&nbsp;based&nbsp;on&nbsp;the&nbsp;current<br>
state.&nbsp;&nbsp;Uses&nbsp;N*&nbsp;and&nbsp;C*&nbsp;for&nbsp;termini.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="ALA-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="ALA-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="ALA-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="ALA-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="ALA-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="ALA-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="ALA-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="ALA-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="ALA-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="ALA-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="ALA-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="ALA-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;C,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="ALA-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="ALA-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="ALA-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="ALA-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="ALA-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="ALA-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="ARG">class <strong>ARG</strong></a>(<a href="src.aa.html#Amino">Amino</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Arginine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Arginine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.aa.html#ARG">ARG</a></dd>
<dd><a href="src.aa.html#Amino">Amino</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="ARG-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="ARG-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;name&nbsp;to&nbsp;use&nbsp;for&nbsp;the&nbsp;forcefield&nbsp;based&nbsp;on&nbsp;the&nbsp;current<br>
state.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.aa.html#Amino">Amino</a>:<br>
<dl><dt><a name="ARG-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="ARG-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="ARG-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Override&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;version&nbsp;of<br>
<a href="#ARG-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list).</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="ARG-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="ARG-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="ARG-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="ARG-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="ARG-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="ARG-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="ARG-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="ARG-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="ARG-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="ARG-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="ARG-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="ARG-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;C,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="ARG-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="ARG-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="ARG-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="ARG-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="ARG-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="ARG-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="ASN">class <strong>ASN</strong></a>(<a href="src.aa.html#Amino">Amino</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Asparagine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Asparagine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.aa.html#ASN">ASN</a></dd>
<dd><a href="src.aa.html#Amino">Amino</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="ASN-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<hr>
Methods inherited from <a href="src.aa.html#Amino">Amino</a>:<br>
<dl><dt><a name="ASN-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="ASN-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="ASN-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Override&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;version&nbsp;of<br>
<a href="#ASN-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list).</tt></dd></dl>

<dl><dt><a name="ASN-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;name&nbsp;to&nbsp;use&nbsp;for&nbsp;the&nbsp;forcefield&nbsp;based&nbsp;on&nbsp;the&nbsp;current<br>
state.&nbsp;&nbsp;Uses&nbsp;N*&nbsp;and&nbsp;C*&nbsp;for&nbsp;termini.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="ASN-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="ASN-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="ASN-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="ASN-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="ASN-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="ASN-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="ASN-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="ASN-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="ASN-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="ASN-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="ASN-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="ASN-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;C,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="ASN-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="ASN-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="ASN-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="ASN-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="ASN-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="ASN-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="ASP">class <strong>ASP</strong></a>(<a href="src.aa.html#Amino">Amino</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Aspartic&nbsp;Acid&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Aspartic&nbsp;Acid&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.aa.html#ASP">ASP</a></dd>
<dd><a href="src.aa.html#Amino">Amino</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="ASP-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="ASP-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;name&nbsp;to&nbsp;use&nbsp;for&nbsp;the&nbsp;forcefield&nbsp;based&nbsp;on&nbsp;the&nbsp;current<br>
state.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.aa.html#Amino">Amino</a>:<br>
<dl><dt><a name="ASP-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="ASP-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="ASP-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Override&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;version&nbsp;of<br>
<a href="#ASP-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list).</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="ASP-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="ASP-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="ASP-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="ASP-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="ASP-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="ASP-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="ASP-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="ASP-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="ASP-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="ASP-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="ASP-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="ASP-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;C,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="ASP-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="ASP-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="ASP-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="ASP-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="ASP-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="ASP-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="Amino">class <strong>Amino</strong></a>(<a href="src.structures.html#Residue">src.structures.Residue</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt><a href="#Amino">Amino</a>&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;provides&nbsp;standard&nbsp;features&nbsp;of&nbsp;the&nbsp;amino&nbsp;acids&nbsp;listed<br>
below<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)<br>
&nbsp;&nbsp;&nbsp;&nbsp;ref:&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;reference&nbsp;object&nbsp;for&nbsp;the&nbsp;amino&nbsp;acid.&nbsp;&nbsp;Used&nbsp;to<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;convert&nbsp;from&nbsp;the&nbsp;alternate&nbsp;naming&nbsp;scheme&nbsp;to&nbsp;the<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;main&nbsp;naming&nbsp;scheme.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Amino-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt></dl>

<dl><dt><a name="Amino-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="Amino-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="Amino-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Override&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;version&nbsp;of<br>
<a href="#Amino-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list).</tt></dd></dl>

<dl><dt><a name="Amino-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;name&nbsp;to&nbsp;use&nbsp;for&nbsp;the&nbsp;forcefield&nbsp;based&nbsp;on&nbsp;the&nbsp;current<br>
state.&nbsp;&nbsp;Uses&nbsp;N*&nbsp;and&nbsp;C*&nbsp;for&nbsp;termini.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="Amino-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="Amino-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="Amino-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="Amino-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="Amino-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="Amino-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="Amino-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="Amino-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="Amino-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="Amino-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="Amino-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="Amino-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;C,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="Amino-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="Amino-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="Amino-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="Amino-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="Amino-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="Amino-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="CYS">class <strong>CYS</strong></a>(<a href="src.aa.html#Amino">Amino</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Cysteine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Cysteine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.aa.html#CYS">CYS</a></dd>
<dd><a href="src.aa.html#Amino">Amino</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="CYS-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="CYS-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;state&nbsp;of&nbsp;the&nbsp;<a href="#CYS">CYS</a>&nbsp;object.&nbsp;&nbsp;If&nbsp;SS-bonded,&nbsp;use&nbsp;CYX.&nbsp;&nbsp;If<br>
negatively&nbsp;charged,&nbsp;use&nbsp;CYM.&nbsp;&nbsp;If&nbsp;HG&nbsp;is&nbsp;not&nbsp;present,&nbsp;use&nbsp;CYX.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.aa.html#Amino">Amino</a>:<br>
<dl><dt><a name="CYS-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="CYS-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="CYS-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Override&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;version&nbsp;of<br>
<a href="#CYS-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list).</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="CYS-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="CYS-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="CYS-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="CYS-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="CYS-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="CYS-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="CYS-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="CYS-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="CYS-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="CYS-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="CYS-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="CYS-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;C,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="CYS-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="CYS-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="CYS-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="CYS-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="CYS-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="CYS-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="GLN">class <strong>GLN</strong></a>(<a href="src.aa.html#Amino">Amino</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Glutamine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Glutamine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.aa.html#GLN">GLN</a></dd>
<dd><a href="src.aa.html#Amino">Amino</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="GLN-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<hr>
Methods inherited from <a href="src.aa.html#Amino">Amino</a>:<br>
<dl><dt><a name="GLN-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="GLN-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="GLN-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Override&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;version&nbsp;of<br>
<a href="#GLN-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list).</tt></dd></dl>

<dl><dt><a name="GLN-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;name&nbsp;to&nbsp;use&nbsp;for&nbsp;the&nbsp;forcefield&nbsp;based&nbsp;on&nbsp;the&nbsp;current<br>
state.&nbsp;&nbsp;Uses&nbsp;N*&nbsp;and&nbsp;C*&nbsp;for&nbsp;termini.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="GLN-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="GLN-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="GLN-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="GLN-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="GLN-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="GLN-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="GLN-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="GLN-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="GLN-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="GLN-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="GLN-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="GLN-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;C,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="GLN-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="GLN-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="GLN-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="GLN-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="GLN-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="GLN-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="GLU">class <strong>GLU</strong></a>(<a href="src.aa.html#Amino">Amino</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Glutamic&nbsp;Acid&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Glutamic&nbsp;Acid&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.aa.html#GLU">GLU</a></dd>
<dd><a href="src.aa.html#Amino">Amino</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="GLU-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="GLU-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;name&nbsp;to&nbsp;use&nbsp;for&nbsp;the&nbsp;forcefield&nbsp;based&nbsp;on&nbsp;the&nbsp;current<br>
state.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.aa.html#Amino">Amino</a>:<br>
<dl><dt><a name="GLU-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="GLU-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="GLU-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Override&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;version&nbsp;of<br>
<a href="#GLU-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list).</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="GLU-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="GLU-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="GLU-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="GLU-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="GLU-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="GLU-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="GLU-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="GLU-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="GLU-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="GLU-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="GLU-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="GLU-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;C,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="GLU-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="GLU-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="GLU-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="GLU-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="GLU-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="GLU-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="GLY">class <strong>GLY</strong></a>(<a href="src.aa.html#Amino">Amino</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Glycine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Glycine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.aa.html#GLY">GLY</a></dd>
<dd><a href="src.aa.html#Amino">Amino</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="GLY-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<hr>
Methods inherited from <a href="src.aa.html#Amino">Amino</a>:<br>
<dl><dt><a name="GLY-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="GLY-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="GLY-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Override&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;version&nbsp;of<br>
<a href="#GLY-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list).</tt></dd></dl>

<dl><dt><a name="GLY-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;name&nbsp;to&nbsp;use&nbsp;for&nbsp;the&nbsp;forcefield&nbsp;based&nbsp;on&nbsp;the&nbsp;current<br>
state.&nbsp;&nbsp;Uses&nbsp;N*&nbsp;and&nbsp;C*&nbsp;for&nbsp;termini.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="GLY-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="GLY-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="GLY-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="GLY-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="GLY-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="GLY-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="GLY-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="GLY-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="GLY-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="GLY-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="GLY-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="GLY-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;C,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="GLY-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="GLY-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="GLY-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="GLY-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="GLY-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="GLY-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="HIS">class <strong>HIS</strong></a>(<a href="src.aa.html#Amino">Amino</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Histidine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Histidine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.aa.html#HIS">HIS</a></dd>
<dd><a href="src.aa.html#Amino">Amino</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="HIS-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="HIS-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Histidines&nbsp;are&nbsp;a&nbsp;special&nbsp;case&nbsp;due&nbsp;to&nbsp;the&nbsp;presence&nbsp;of<br>
several&nbsp;different&nbsp;forms.&nbsp;&nbsp;This&nbsp;function&nbsp;sets&nbsp;all&nbsp;non-<br>
positive&nbsp;incarnations&nbsp;of&nbsp;<a href="#HIS">HIS</a>&nbsp;to&nbsp;neutral&nbsp;<a href="#HIS">HIS</a>&nbsp;by<br>
checking&nbsp;to&nbsp;see&nbsp;if&nbsp;optimization&nbsp;removed&nbsp;hacceptor&nbsp;or<br>
hdonor&nbsp;flags.&nbsp;&nbsp;Otherwise&nbsp;HID&nbsp;is&nbsp;used&nbsp;as&nbsp;the&nbsp;default.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.aa.html#Amino">Amino</a>:<br>
<dl><dt><a name="HIS-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="HIS-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="HIS-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Override&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;version&nbsp;of<br>
<a href="#HIS-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list).</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="HIS-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="HIS-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="HIS-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="HIS-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="HIS-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="HIS-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="HIS-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="HIS-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="HIS-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="HIS-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="HIS-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="HIS-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;C,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="HIS-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="HIS-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="HIS-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="HIS-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="HIS-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="HIS-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="ILE">class <strong>ILE</strong></a>(<a href="src.aa.html#Amino">Amino</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Isoleucine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Isoleucine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.aa.html#ILE">ILE</a></dd>
<dd><a href="src.aa.html#Amino">Amino</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="ILE-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<hr>
Methods inherited from <a href="src.aa.html#Amino">Amino</a>:<br>
<dl><dt><a name="ILE-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="ILE-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="ILE-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Override&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;version&nbsp;of<br>
<a href="#ILE-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list).</tt></dd></dl>

<dl><dt><a name="ILE-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;name&nbsp;to&nbsp;use&nbsp;for&nbsp;the&nbsp;forcefield&nbsp;based&nbsp;on&nbsp;the&nbsp;current<br>
state.&nbsp;&nbsp;Uses&nbsp;N*&nbsp;and&nbsp;C*&nbsp;for&nbsp;termini.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="ILE-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="ILE-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="ILE-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="ILE-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="ILE-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="ILE-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="ILE-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="ILE-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="ILE-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="ILE-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="ILE-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="ILE-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;C,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="ILE-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="ILE-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="ILE-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="ILE-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="ILE-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="ILE-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="LEU">class <strong>LEU</strong></a>(<a href="src.aa.html#Amino">Amino</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Leucine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Leucine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.aa.html#LEU">LEU</a></dd>
<dd><a href="src.aa.html#Amino">Amino</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="LEU-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<hr>
Methods inherited from <a href="src.aa.html#Amino">Amino</a>:<br>
<dl><dt><a name="LEU-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="LEU-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="LEU-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Override&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;version&nbsp;of<br>
<a href="#LEU-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list).</tt></dd></dl>

<dl><dt><a name="LEU-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;name&nbsp;to&nbsp;use&nbsp;for&nbsp;the&nbsp;forcefield&nbsp;based&nbsp;on&nbsp;the&nbsp;current<br>
state.&nbsp;&nbsp;Uses&nbsp;N*&nbsp;and&nbsp;C*&nbsp;for&nbsp;termini.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="LEU-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="LEU-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="LEU-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="LEU-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="LEU-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="LEU-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="LEU-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="LEU-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="LEU-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="LEU-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="LEU-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="LEU-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;C,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="LEU-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="LEU-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="LEU-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="LEU-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="LEU-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="LEU-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="LIG">class <strong>LIG</strong></a>(<a href="src.structures.html#Residue">src.structures.Residue</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Generic&nbsp;ligand&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;generic&nbsp;ligand&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="LIG-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="LIG-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="LIG-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;a&nbsp;water&nbsp;atom.&nbsp;&nbsp;Note&nbsp;the&nbsp;HETATM&nbsp;field.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;&nbsp;The&nbsp;new&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list)</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="LIG-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="LIG-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="LIG-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="LIG-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="LIG-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="LIG-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="LIG-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="LIG-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="LIG-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="LIG-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="LIG-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="LIG-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;C,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="LIG-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="LIG-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="LIG-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="LIG-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="LIG-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="LIG-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="LYS">class <strong>LYS</strong></a>(<a href="src.aa.html#Amino">Amino</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Lysine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Lysine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.aa.html#LYS">LYS</a></dd>
<dd><a href="src.aa.html#Amino">Amino</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="LYS-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="LYS-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Determine&nbsp;if&nbsp;this&nbsp;is&nbsp;LYN&nbsp;or&nbsp;not</tt></dd></dl>

<hr>
Methods inherited from <a href="src.aa.html#Amino">Amino</a>:<br>
<dl><dt><a name="LYS-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="LYS-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="LYS-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Override&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;version&nbsp;of<br>
<a href="#LYS-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list).</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="LYS-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="LYS-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="LYS-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="LYS-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="LYS-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="LYS-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="LYS-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="LYS-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="LYS-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="LYS-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="LYS-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="LYS-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;C,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="LYS-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="LYS-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="LYS-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="LYS-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="LYS-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="LYS-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="MET">class <strong>MET</strong></a>(<a href="src.aa.html#Amino">Amino</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Methionine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Methionine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.aa.html#MET">MET</a></dd>
<dd><a href="src.aa.html#Amino">Amino</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="MET-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<hr>
Methods inherited from <a href="src.aa.html#Amino">Amino</a>:<br>
<dl><dt><a name="MET-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="MET-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="MET-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Override&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;version&nbsp;of<br>
<a href="#MET-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list).</tt></dd></dl>

<dl><dt><a name="MET-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;name&nbsp;to&nbsp;use&nbsp;for&nbsp;the&nbsp;forcefield&nbsp;based&nbsp;on&nbsp;the&nbsp;current<br>
state.&nbsp;&nbsp;Uses&nbsp;N*&nbsp;and&nbsp;C*&nbsp;for&nbsp;termini.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="MET-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="MET-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="MET-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="MET-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="MET-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="MET-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="MET-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="MET-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="MET-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="MET-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="MET-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="MET-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;C,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="MET-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="MET-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="MET-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="MET-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="MET-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="MET-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="PHE">class <strong>PHE</strong></a>(<a href="src.aa.html#Amino">Amino</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Phenylalanine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Phenylalanine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.aa.html#PHE">PHE</a></dd>
<dd><a href="src.aa.html#Amino">Amino</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="PHE-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<hr>
Methods inherited from <a href="src.aa.html#Amino">Amino</a>:<br>
<dl><dt><a name="PHE-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="PHE-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="PHE-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Override&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;version&nbsp;of<br>
<a href="#PHE-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list).</tt></dd></dl>

<dl><dt><a name="PHE-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;name&nbsp;to&nbsp;use&nbsp;for&nbsp;the&nbsp;forcefield&nbsp;based&nbsp;on&nbsp;the&nbsp;current<br>
state.&nbsp;&nbsp;Uses&nbsp;N*&nbsp;and&nbsp;C*&nbsp;for&nbsp;termini.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="PHE-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="PHE-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="PHE-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="PHE-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="PHE-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="PHE-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="PHE-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="PHE-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="PHE-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="PHE-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="PHE-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="PHE-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;C,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="PHE-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="PHE-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="PHE-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="PHE-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="PHE-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="PHE-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="PRO">class <strong>PRO</strong></a>(<a href="src.aa.html#Amino">Amino</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Proline&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Proline&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.aa.html#PRO">PRO</a></dd>
<dd><a href="src.aa.html#Amino">Amino</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="PRO-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="PRO-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;name&nbsp;to&nbsp;use&nbsp;for&nbsp;the&nbsp;forcefield&nbsp;based&nbsp;on&nbsp;the&nbsp;current<br>
state.&nbsp;&nbsp;Uses&nbsp;N*&nbsp;and&nbsp;C*&nbsp;for&nbsp;termini.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.aa.html#Amino">Amino</a>:<br>
<dl><dt><a name="PRO-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="PRO-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="PRO-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Override&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;version&nbsp;of<br>
<a href="#PRO-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list).</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="PRO-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="PRO-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="PRO-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="PRO-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="PRO-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="PRO-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="PRO-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="PRO-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="PRO-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="PRO-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="PRO-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="PRO-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;C,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="PRO-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="PRO-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="PRO-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="PRO-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="PRO-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="PRO-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="SER">class <strong>SER</strong></a>(<a href="src.aa.html#Amino">Amino</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Serine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Serine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.aa.html#SER">SER</a></dd>
<dd><a href="src.aa.html#Amino">Amino</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="SER-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<hr>
Methods inherited from <a href="src.aa.html#Amino">Amino</a>:<br>
<dl><dt><a name="SER-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="SER-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="SER-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Override&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;version&nbsp;of<br>
<a href="#SER-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list).</tt></dd></dl>

<dl><dt><a name="SER-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;name&nbsp;to&nbsp;use&nbsp;for&nbsp;the&nbsp;forcefield&nbsp;based&nbsp;on&nbsp;the&nbsp;current<br>
state.&nbsp;&nbsp;Uses&nbsp;N*&nbsp;and&nbsp;C*&nbsp;for&nbsp;termini.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="SER-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="SER-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="SER-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="SER-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="SER-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="SER-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="SER-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="SER-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="SER-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="SER-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="SER-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="SER-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;C,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="SER-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="SER-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="SER-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="SER-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="SER-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="SER-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="THR">class <strong>THR</strong></a>(<a href="src.aa.html#Amino">Amino</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Threonine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Threonine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.aa.html#THR">THR</a></dd>
<dd><a href="src.aa.html#Amino">Amino</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="THR-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<hr>
Methods inherited from <a href="src.aa.html#Amino">Amino</a>:<br>
<dl><dt><a name="THR-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="THR-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="THR-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Override&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;version&nbsp;of<br>
<a href="#THR-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list).</tt></dd></dl>

<dl><dt><a name="THR-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;name&nbsp;to&nbsp;use&nbsp;for&nbsp;the&nbsp;forcefield&nbsp;based&nbsp;on&nbsp;the&nbsp;current<br>
state.&nbsp;&nbsp;Uses&nbsp;N*&nbsp;and&nbsp;C*&nbsp;for&nbsp;termini.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="THR-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="THR-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="THR-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="THR-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="THR-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="THR-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="THR-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="THR-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="THR-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="THR-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="THR-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="THR-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;C,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="THR-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="THR-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="THR-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="THR-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="THR-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="THR-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="TRP">class <strong>TRP</strong></a>(<a href="src.aa.html#Amino">Amino</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Tryptophan&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Tryptophan&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.aa.html#TRP">TRP</a></dd>
<dd><a href="src.aa.html#Amino">Amino</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="TRP-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<hr>
Methods inherited from <a href="src.aa.html#Amino">Amino</a>:<br>
<dl><dt><a name="TRP-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="TRP-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="TRP-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Override&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;version&nbsp;of<br>
<a href="#TRP-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list).</tt></dd></dl>

<dl><dt><a name="TRP-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;name&nbsp;to&nbsp;use&nbsp;for&nbsp;the&nbsp;forcefield&nbsp;based&nbsp;on&nbsp;the&nbsp;current<br>
state.&nbsp;&nbsp;Uses&nbsp;N*&nbsp;and&nbsp;C*&nbsp;for&nbsp;termini.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="TRP-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="TRP-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="TRP-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="TRP-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="TRP-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="TRP-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="TRP-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="TRP-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="TRP-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="TRP-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="TRP-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="TRP-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;C,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="TRP-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="TRP-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="TRP-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="TRP-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="TRP-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="TRP-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="TYR">class <strong>TYR</strong></a>(<a href="src.aa.html#Amino">Amino</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Tyrosine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Tyrosine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.aa.html#TYR">TYR</a></dd>
<dd><a href="src.aa.html#Amino">Amino</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="TYR-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="TYR-setState"><strong>setState</strong></a>(self)</dt><dd><tt>See&nbsp;if&nbsp;the&nbsp;<a href="#TYR">TYR</a>&nbsp;is&nbsp;negative&nbsp;or&nbsp;not</tt></dd></dl>

<hr>
Methods inherited from <a href="src.aa.html#Amino">Amino</a>:<br>
<dl><dt><a name="TYR-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="TYR-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="TYR-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Override&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;version&nbsp;of<br>
<a href="#TYR-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list).</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="TYR-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="TYR-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="TYR-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="TYR-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="TYR-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="TYR-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="TYR-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="TYR-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="TYR-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="TYR-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="TYR-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="TYR-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;C,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="TYR-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="TYR-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="TYR-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="TYR-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="TYR-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="TYR-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="VAL">class <strong>VAL</strong></a>(<a href="src.aa.html#Amino">Amino</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Valine&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Valine&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.aa.html#VAL">VAL</a></dd>
<dd><a href="src.aa.html#Amino">Amino</a></dd>
<dd><a href="src.structures.html#Residue">src.structures.Residue</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="VAL-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<hr>
Methods inherited from <a href="src.aa.html#Amino">Amino</a>:<br>
<dl><dt><a name="VAL-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="VAL-addDihedralAngle"><strong>addDihedralAngle</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;chiangles<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;value&nbsp;to&nbsp;be&nbsp;added&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="VAL-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;an&nbsp;atom.&nbsp;&nbsp;Override&nbsp;the&nbsp;generic&nbsp;residue's&nbsp;version&nbsp;of<br>
<a href="#VAL-createAtom">createAtom</a>().<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;The&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list).</tt></dd></dl>

<dl><dt><a name="VAL-setState"><strong>setState</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;name&nbsp;to&nbsp;use&nbsp;for&nbsp;the&nbsp;forcefield&nbsp;based&nbsp;on&nbsp;the&nbsp;current<br>
state.&nbsp;&nbsp;Uses&nbsp;N*&nbsp;and&nbsp;C*&nbsp;for&nbsp;termini.</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="VAL-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="VAL-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="VAL-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="VAL-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="VAL-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="VAL-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="VAL-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="VAL-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="VAL-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="VAL-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="VAL-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="VAL-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;C,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="VAL-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="VAL-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="VAL-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="VAL-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="VAL-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="VAL-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="WAT">class <strong>WAT</strong></a>(<a href="src.structures.html#Residue">src.structures.Residue</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Water&nbsp;class<br>
&nbsp;<br>
This&nbsp;class&nbsp;gives&nbsp;data&nbsp;about&nbsp;the&nbsp;Water&nbsp;object,&nbsp;and&nbsp;inherits<br>
off&nbsp;the&nbsp;base&nbsp;residue&nbsp;class.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="WAT-__init__"><strong>__init__</strong></a>(self, atoms, ref)</dt><dd><tt>Initialize&nbsp;the&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A&nbsp;list&nbsp;of&nbsp;Atom&nbsp;objects&nbsp;to&nbsp;be&nbsp;stored&nbsp;in&nbsp;this&nbsp;class<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(list)</tt></dd></dl>

<dl><dt><a name="WAT-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Override&nbsp;the&nbsp;existing&nbsp;addAtom&nbsp;-&nbsp;include&nbsp;the&nbsp;link&nbsp;to&nbsp;the<br>
reference&nbsp;object</tt></dd></dl>

<dl><dt><a name="WAT-createAtom"><strong>createAtom</strong></a>(self, atomname, newcoords)</dt><dd><tt>Create&nbsp;a&nbsp;water&nbsp;atom.&nbsp;&nbsp;Note&nbsp;the&nbsp;HETATM&nbsp;field.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newcoords:&nbsp;&nbsp;The&nbsp;new&nbsp;coordinates&nbsp;of&nbsp;the&nbsp;atom&nbsp;(list)</tt></dd></dl>

<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="WAT-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Basic&nbsp;string&nbsp;representation&nbsp;for&nbsp;debugging</tt></dd></dl>

<dl><dt><a name="WAT-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add&nbsp;the&nbsp;value&nbsp;to&nbsp;the&nbsp;list&nbsp;of&nbsp;missing&nbsp;atoms<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;missing&nbsp;atom&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="WAT-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;member&nbsp;(string)<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chainID:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;missing:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;List&nbsp;of&nbsp;missing&nbsp;atoms&nbsp;of&nbsp;the&nbsp;residue<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="WAT-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;mapping<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;resname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue&nbsp;to&nbsp;retrieve&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="WAT-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>

<dl><dt><a name="WAT-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;total&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue.&nbsp;&nbsp;In&nbsp;order&nbsp;to&nbsp;get&nbsp;rid<br>
of&nbsp;floating&nbsp;point&nbsp;rounding&nbsp;error,&nbsp;do&nbsp;the&nbsp;string<br>
transformation.<br>
&nbsp;<br>
Returns:<br>
&nbsp;&nbsp;&nbsp;&nbsp;charge:&nbsp;The&nbsp;charge&nbsp;of&nbsp;the&nbsp;residue&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="WAT-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>

<dl><dt><a name="WAT-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;for&nbsp;the&nbsp;residue<br>
&nbsp;<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;count:&nbsp;&nbsp;Number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="WAT-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove&nbsp;an&nbsp;atom&nbsp;from&nbsp;the&nbsp;residue&nbsp;object.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;atomname:&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;atom&nbsp;to&nbsp;be&nbsp;removed&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="WAT-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename&nbsp;an&nbsp;atom&nbsp;to&nbsp;a&nbsp;new&nbsp;name<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;oldname:&nbsp;The&nbsp;old&nbsp;atom&nbsp;name&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;newname:&nbsp;The&nbsp;new&nbsp;atom&nbsp;name&nbsp;(string)</tt></dd></dl>

<dl><dt><a name="WAT-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename&nbsp;a&nbsp;given&nbsp;residue<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;new&nbsp;name&nbsp;of&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="WAT-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder&nbsp;the&nbsp;atoms&nbsp;to&nbsp;start&nbsp;with&nbsp;N,&nbsp;CA,&nbsp;C,&nbsp;O&nbsp;if&nbsp;they&nbsp;exist</tt></dd></dl>

<dl><dt><a name="WAT-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate&nbsp;about&nbsp;the&nbsp;atom1-atom2&nbsp;bond&nbsp;by&nbsp;a&nbsp;given&nbsp;angle<br>
All&nbsp;atoms&nbsp;connected&nbsp;to&nbsp;atom2&nbsp;will&nbsp;rotate.<br>
&nbsp;<br>
Parameters:<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom1:&nbsp;&nbsp;The&nbsp;first&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;atom2:&nbsp;&nbsp;The&nbsp;second&nbsp;atom&nbsp;of&nbsp;the&nbsp;bond&nbsp;to&nbsp;rotate&nbsp;about&nbsp;(atom)<br>
&nbsp;&nbsp;&nbsp;&nbsp;angle:&nbsp;&nbsp;The&nbsp;number&nbsp;of&nbsp;degrees&nbsp;to&nbsp;rotate&nbsp;(float)</tt></dd></dl>

<dl><dt><a name="WAT-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;a&nbsp;member&nbsp;of&nbsp;the&nbsp;<a href="src.structures.html#Residue">Residue</a>&nbsp;class&nbsp;to&nbsp;a&nbsp;specific&nbsp;value&nbsp;<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;object&nbsp;to&nbsp;set&nbsp;(string)<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;object&nbsp;to&nbsp;append<br>
Possible&nbsp;Values<br>
&nbsp;&nbsp;&nbsp;&nbsp;atoms:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;atoms&nbsp;in&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;name:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;name&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;chain:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;chainID&nbsp;associated&nbsp;with&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;sequence&nbsp;number&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;icode:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;iCode&nbsp;of&nbsp;the&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbonded:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;has&nbsp;a&nbsp;SS&nbsp;bond,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;SSbondpartner:&nbsp;The&nbsp;residue&nbsp;of&nbsp;the&nbsp;bond&nbsp;partner<br>
&nbsp;&nbsp;&nbsp;&nbsp;type:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;type&nbsp;associated&nbsp;with&nbsp;this&nbsp;residue<br>
&nbsp;&nbsp;&nbsp;&nbsp;isNterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;#&nbsp;of&nbsp;hydrogens&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;N-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isCterm:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;the&nbsp;C-Terminus,&nbsp;0&nbsp;otherwise<br>
&nbsp;&nbsp;&nbsp;&nbsp;isDirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1&nbsp;if&nbsp;the&nbsp;residue&nbsp;is&nbsp;not&nbsp;missing&nbsp;atoms,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;0&nbsp;otherwise<br>
Notes<br>
&nbsp;&nbsp;&nbsp;&nbsp;resSeq&nbsp;points&nbsp;to&nbsp;the&nbsp;residue.setResSeq&nbsp;function<br>
Returns<br>
&nbsp;&nbsp;&nbsp;&nbsp;item:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The&nbsp;value&nbsp;of&nbsp;the&nbsp;member</tt></dd></dl>

<dl><dt><a name="WAT-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;chainID&nbsp;field&nbsp;to&nbsp;a&nbsp;certain&nbsp;value</tt></dd></dl>

<dl><dt><a name="WAT-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set&nbsp;the&nbsp;donors&nbsp;and&nbsp;acceptors&nbsp;within&nbsp;the&nbsp;residue</tt></dd></dl>

<dl><dt><a name="WAT-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set&nbsp;the&nbsp;atom&nbsp;field&nbsp;resSeq&nbsp;to&nbsp;a&nbsp;certain&nbsp;value&nbsp;and<br>
change&nbsp;the&nbsp;residue's&nbsp;information.&nbsp;&nbsp;The&nbsp;icode&nbsp;field&nbsp;is&nbsp;no&nbsp;longer<br>
useful.<br>
&nbsp;<br>
Parameters<br>
&nbsp;&nbsp;&nbsp;&nbsp;value:&nbsp;&nbsp;The&nbsp;new&nbsp;value&nbsp;of&nbsp;resSeq&nbsp;(int)</tt></dd></dl>

<dl><dt><a name="WAT-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update&nbsp;the&nbsp;isNterms&nbsp;and&nbsp;isCterm&nbsp;flags</tt></dd></dl>

</td></tr></table></td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#55aa55">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Data</strong></big></font></td></tr>
    
<tr><td bgcolor="#55aa55"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%"><strong>BACKBONE</strong> = ['N', 'CA', 'C', 'O', 'O2', 'HA', 'HN', 'H', 'tN']<br>
<strong>DIHEDRAL</strong> = 57.2958<br>
<strong>SMALL</strong> = 9.9999999999999995e-08<br>
<strong>__author__</strong> = 'Todd Dolinsky'<br>
<strong>__date__</strong> = '28 December 2006'</td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#7799ee">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Author</strong></big></font></td></tr>
    
<tr><td bgcolor="#7799ee"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%">Todd&nbsp;Dolinsky</td></tr></table>
</body></html>